Summary: This report explores adult fish passage recorded from 2001-01-01 to 2010-12-31 at the Willamette Falls fish ladder on the Willamette River, Oregon. This report is focused on Coho, Jack Coho, and Steelhead species. First, a time series graph visualized time series data by month and year to explore trends over the 10-year time period. Second, a season plot is created to explore seasonal trends for each species. Lastly, a total counts figure illustrates the total number of observed fish passage for each species over the 10-year period.
Image of Willamette Falls, OR:
knitr::include_graphics('willamette_falls.jpeg')
Photo of Willamette Falls, Oregon. Credit: EncMstr, CC BY-SA 3.0 http://creativecommons.org/licenses/by-sa/3.0/, via Wikimedia Commons
Map of Willamette Falls, OR:
knitr::include_graphics('willamette_falls_map.png')
Map of the location of the fish ladder in Willamette Falls, Oregon. Credit: Google Maps
Data Source: University of Washington. (n.d.). DART Adult Passage Graphics & Text. Columbia Basin Research. http://www.cbr.washington.edu/dart/query/adult_graph_text
## Read in packages
library(tidyverse)
library(here)
library(janitor)
library(lubridate)
library(tsibble)
## Read in the data, keep only the columns of interest, replace "NA" with 0, and clean names
fish_af <- read.csv(here("data", "willamette_fish_passage.csv")) %>%
select("Date", "Coho", "Jack.Coho", "Steelhead") %>%
mutate_all(~replace(., is.na(.), 0)) %>%
clean_names()
## Convert to tsibble
fish_ts <- fish_af %>%
mutate(date = lubridate::mdy(date)) %>%
as_tsibble(key = NULL, index = date)
## Plot the time series data
# ggplot() +
# geom_line(data = fish_ts, aes(x = date, y = coho)) +
# labs(x = "Date",
# y = "Number of Coho")
## Make data frames for each fish by monthyears
coho_month <- fish_ts %>%
index_by(yr_mo = ~yearmonth(.)) %>%
summarize(monthly_mean_coho = mean(coho, na.rm = TRUE))
jack_month <- fish_ts %>%
index_by(yr_mo = ~yearmonth(.)) %>%
summarize(monthly_mean_jack = mean(jack_coho, na.rm = TRUE))
steel_month <- fish_ts %>%
index_by(yr_mo = ~yearmonth(.)) %>%
summarize(monthly_mean_steel = mean(steelhead, na.rm = TRUE))
## Plot time series fish passage for the three species with month/year data
ggplot() +
geom_line(data = coho_month,
aes(x = yr_mo,
y = monthly_mean_coho,
colour = "Coho"),
alpha = 0.8,
size = 1) +
geom_line(data = jack_month,
aes(x = yr_mo,
y = monthly_mean_jack,
colour = "Jack Coho"),
alpha = 0.8,
size = 1) +
geom_line(data = steel_month,
aes(x = yr_mo,
y = monthly_mean_steel,
colour = "Steelhead"),
alpha = 0.8,
size = 1) +
labs(x = "Month and Year",
y = "Number of Fish Observed",
colour = "Species",
title = "Adult Passage of Coho, Jack Coho, and Steelhead at Willamette Falls") +
theme_minimal() +
scale_colour_manual(values = c("dodgerblue4", "darkorchid4", "springgreen4"))
Figure 1.1 Time series plot of Coho, Jack Coho, and Steelhead adult fish passage at the Willamette Falls fish ladder between 2001 and 2010, plotting the average fish numbers for each month. Data were shared by and accessed from Columbia River DART (Data Access in Real Time).
Summary
# Attach feasts package
library(feasts)
# Pivot longer
fish_ts_longer <- fish_ts %>%
pivot_longer(2:4,
names_to = "species", # Move each species to its own column
values_to = "n") %>%
group_by(species) %>% # Group by species
mutate(species = case_when(
species == "coho" ~ "Coho",
species == "jack_coho" ~ "Jack Coho",
species == "steelhead" ~ "Steelhead")
) %>%
index_by(yr_mo = ~yearmonth(.)) %>% # Group by year & month
summarize(monthly_mean = mean(n, na.rm = TRUE)) # Summarize the mean for each species for each month
# Make vector for species color
fish_color = c("Coho" = "dodgerblue4", "Jack Coho" = "darkorchid4", "Steelhead" = "springgreen4")
# Make seasonplot
fish_ts_longer %>%
gg_season(y = monthly_mean) +
labs(x = "Month",
y = "Mean Number of Fish Observed",
colour = "Year",
title = "Seasonal Adult Passage of Coho, Jack Coho, and Steelhead at Willamette Falls") +
theme_minimal() +
theme(
strip.background = element_rect(color = fish_color,
fill = fish_color),
strip.text = element_text(color = "white")
)
Figure 1.2 Passage of Coho, Jack Coho, and Steelhead at Willamette Falls for all years between 2001 and 2010, plotted to show the seasonality. Data were shared by and accessed from Columbia River DART (Data Access in Real Time).
Summary
The mean counts for Coho and Jack Coho peak during the months of August to October, while the mean count for Steelhead peak around May and June.
Coho had the highest peak mean count during the years 2009 and 2010. Jack Coho has the highest peak mean count during the year 2008. Steelhead had higher peak mean counts during the years 2002-2004.
## Make data frames for each fish species by year
coho_year <- fish_ts %>%
index_by(yr = ~year(.)) %>%
summarize(year_count_coho = sum(coho, na.rm = TRUE))
jack_year <- fish_ts %>%
index_by(yr = ~year(.)) %>%
summarize(year_count_jack = sum(jack_coho, na.rm = TRUE))
steel_year <- fish_ts %>%
index_by(yr = ~year(.)) %>%
summarize(year_count_steel = sum(steelhead, na.rm = TRUE))
jack_year <- fish_ts %>%
index_by(yr = ~year(.)) %>%
summarize(year_count_jack = sum(jack_coho, na.rm = TRUE))
steel_year <- fish_ts %>%
index_by(yr = ~year(.)) %>%
summarize(year_count_steel = sum(steelhead, na.rm = TRUE))
## Plot annual totals for fish passage, for each of the 3 species
ggplot() +
geom_line(data = coho_year,
aes(x = yr,
y = year_count_coho,
colour = "Coho"),
alpha = 0.7,
size = 1.2) +
geom_line(data = jack_year,
aes(x = yr,
y = year_count_jack,
colour = "Jack Coho"),
alpha = 0.7,
size = 1.2) +
geom_line(data = steel_year,
aes(x = yr,
y = year_count_steel,
colour = "Steelhead"),
alpha = 0.7,
size = 1.2) +
scale_x_continuous(breaks= c(2000,2001,2002,2003,2004,2005,2006,2007,2008,2009,2010)) +
labs(x = "Year",
y = "Number of Fish",
colour = "Species",
title = "Annual Adult Passage of Coho, Jack Coho, and Steelhead at Willamette Falls") +
theme_minimal() +
scale_colour_manual(values = c("dodgerblue4", "darkorchid4", "springgreen4"))
Figure 1.3 Annual total Coho, Jack Coho, and Steelhead passage observations were recorded at the Willamette Falls fish ladder on the Willamette River (Oregon) from 2001-2010. Data were shared by and accessed from Columbia River DART (Data Access in Real Time).
Summary
From 2001 to 2010, Steelhead observations showed a steady decline, with a small rebound between 2009-2010.
Coho observations increased drastically, from ~5,000/year to ~25,000/year in 2009.
Jack Coho observations remained relatively consistent over the 10-year period.